8E24 | pdb_00008e24

Human DNA polymerase theta in complex with allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8E24

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta.

Bubenik, M.Mader, P.Mochirian, P.Vallee, F.Clark, J.Truchon, J.F.Perryman, A.L.Pau, V.Kurinov, I.Zahn, K.E.Leclaire, M.E.Papp, R.Mathieu, M.C.Hamel, M.Duffy, N.M.Godbout, C.Casas-Selves, M.Falgueyret, J.P.Baruah, P.S.Nicolas, O.Stocco, R.Poirier, H.Martino, G.Fortin, A.B.Roulston, A.Chefson, A.Dorich, S.St-Onge, M.Patel, P.Pellerin, C.Ciblat, S.Pinter, T.Barabe, F.El Bakkouri, M.Parikh, P.Gervais, C.Sfeir, A.Mamane, Y.Morris, S.J.Black, W.C.Sicheri, F.Gallant, M.

(2022) J Med Chem 65: 13198-13215

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00998
  • Primary Citation Related Structures: 
    8E23, 8E24

  • PubMed Abstract: 

    DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685 : a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2 -/- mouse tumor xenograft model.


  • Organizational Affiliation
    • Repare Therapeutics, 7171 Frederick-Banting, Building 2, Montréal, Québec H4S 1Z9, Canada.

Macromolecule Content 

  • Total Structure Weight: 170.67 kDa 
  • Atom Count: 11,101 
  • Modeled Residue Count: 1,338 
  • Deposited Residue Count: 1,396 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase theta
A, D
668Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 2.7.7.7 (PDB Primary Data), 3.6.4.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens)
Explore O75417 
Go to UniProtKB:  O75417
PHAROS:  O75417
GTEx:  ENSG00000051341 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75417
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA
B, E
17synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA
C, F
13synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG3

Query on DG3



Download:Ideal Coordinates CCD File
H [auth A],
K [auth D]
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
UA6
(Subject of Investigation/LOI)

Query on UA6



Download:Ideal Coordinates CCD File
I [auth A],
L [auth D]
2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide
C23 H15 F6 N3 O
SCSRPWBBDHKGCX-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UA6 BindingDB:  8E24 IC50: 1.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.739α = 90
b = 66.287β = 126.14
c = 156.662γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN 143277
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description